grch38-canonical-transcript-features-gencode-v1¶
Protein Coding Canonical Transcript Features for each protein coding gene id from GENCODE's v34 (Ensembl 100) comprehensive set of gene anntotations. Canonical Transcripts are determined using the APPRIS annotation dataset. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene are not annotated by APPRIS, the transcript with the most exons is chosen as the canonical transcript. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine.
GGD Package |
grch38-canonical-transcript-features-gencode-v1 |
Species |
Homo_sapiens |
Genome Build |
GRCh38 |
GGD Channel |
ggd-genomics |
Package Version |
1 |
Recipe Author |
mjc |
Data Provider |
GENCODE |
Data Version |
release-34_03-24-2020 |
Genomic File Type |
gtf |
Data file coordinate basing |
1-based-inclusive |
Package’s Data Files |
grch38-canonical-transcript-features-gencode-v1.gtf.gz, grch38-canonical-transcript-features-gencode-v1.gtf.gz.tbi |
Approximate Size of Each Data File |
grch38-canonical-transcript-features-gencode-v1.gtf.gz: 10.74M, grch38-canonical-transcript-features-gencode-v1.gtf.gz.tbi: 262.63K |
Package Keywords |
Canonical, Canonical-Transcripts, Canonical-Isoforms, Gene-Features, GTF, Gene-Features, Gene-Annotations, GTF, GENOCDOE-GTF, GENCODE-Gene-Sets, Annotated-Transcripts |
Package Dependencies: |
gsort, htslib, zlib |
Recipe |
Install with --prefix
¶
Prefix install enabled: True
Installation¶
With ggd installed and an activated ggd channel (see Using GGD), install with:
ggd install -c genomics grch38-canonical-transcript-features-gencode-v1
Activating Environment Variables¶
Run source activate base
after installing the data package to activate the environment variables
associated with this data package.
Note
You must be in the conda environment where the data package was installed in order to use the
associated environment variables. Otherwise, use ggd get-files
to access this package’s
data files.